HMCN2 hemicentin 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HMCN2provided by HGNC
Official Full Name: hemicentin 2provided by HGNC
Primary source: HGNC:HGNC:21293
See related: Ensembl:ENSG00000148357 AllianceGenome:HGNC:21293
Gene type: protein coding
RefSeq status: INFERRED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: Predicted to enable axon guidance receptor activity. Predicted to be involved in homophilic cell adhesion via plasma membrane adhesion molecules and synapse organization. Located in collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Broad expression in small intestine (RPKM 2.1), fat (RPKM 1.8) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q34.11

Exon count:: 102

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (130265760..130434123)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (142470624..142639100)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (133028039..133309510)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of hemicentin 2 (HMCN2) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed
Knockdown of hemicentin 2 (HMCN2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-153301 (e-PCR)
- UniSTS:177665

SHGC-147269 (e-PCR)
- UniSTS:175710

D15S1477 (e-PCR)
- UniSTS:474482

SHGC-147754 (e-PCR)
- UniSTS:175988

D1S3693 (e-PCR)
- UniSTS:474271

Clone Names

FLJ23816, FLJ46139, FLJ46844, DKFZp434P0216

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables axon guidance receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables extracellular matrix structural constituent	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in axon guidance	IEA Inferred from Electronic Annotation more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IBA Inferred from Biological aspect of Ancestor more info
involved_in synapse organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in basement membrane	IEA Inferred from Electronic Annotation more info
located_in cell cortex	IEA Inferred from Electronic Annotation more info
located_in cell junction	IEA Inferred from Electronic Annotation more info
located_in cleavage furrow	IEA Inferred from Electronic Annotation more info
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in neuronal cell body	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: hemicentin-2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001291815.2 → NP_001278744.1 hemicentin-2 precursor

Status: INFERRED

Source sequence(s)

ABBA01012042, ABBA01043973, AL354898, AL360004, FP565345, KF458942

Consensus CDS

CCDS94512.1

UniProtKB/Swiss-Prot

A0A096LP30, A0A804HLC3, Q8N225, Q8NDA2, Q8TCI8

Related

ENSP00000508292.2, ENST00000683500.2

Conserved Domains (11) summary

cd00096
Location:1912 → 1975

Ig; Immunoglobulin domain

smart00408
Location:4247 → 4309

IGc2; Immunoglobulin C-2 Type

smart00179
Location:4883 → 4922

EGF_CA; Calcium-binding EGF-like domain

smart00409
Location:792 → 879

IG; Immunoglobulin

smart00410
Location:2954 → 3034

IG_like; Immunoglobulin like

pfam07679
Location:4323 → 4409

I-set; Immunoglobulin I-set domain

pfam07474
Location:4411 → 4593

G2F; G2F domain

pfam07645
Location:4733 → 4774

EGF_CA; Calcium-binding EGF domain

pfam13519
Location:39 → 209

VWA_2; von Willebrand factor type A domain

pfam14670
Location:4652 → 4687

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl11960
Location:4322 → 4405

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

130265760..130434123

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011518466.3 → XP_011516768.1 hemicentin-2 isoform X2

Conserved Domains (11) summary

cd00096
Location:1912 → 1975

Ig; Immunoglobulin domain

smart00408
Location:4247 → 4309

IGc2; Immunoglobulin C-2 Type

smart00179
Location:4839 → 4878

EGF_CA; Calcium-binding EGF-like domain

smart00409
Location:792 → 879

IG; Immunoglobulin

smart00410
Location:2954 → 3034

IG_like; Immunoglobulin like

pfam07679
Location:4323 → 4409

I-set; Immunoglobulin I-set domain

pfam07474
Location:4411 → 4593

G2F; G2F domain

pfam07645
Location:4689 → 4730

EGF_CA; Calcium-binding EGF domain

pfam13519
Location:39 → 209

VWA_2; von Willebrand factor type A domain

pfam14670
Location:4652 → 4687

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl11960
Location:4322 → 4405

Ig; Immunoglobulin domain
XM_011518465.3 → XP_011516767.1 hemicentin-2 isoform X1

Conserved Domains (10) summary

cd00096
Location:1912 → 1975

Ig; Immunoglobulin domain

smart00408
Location:4247 → 4309

IGc2; Immunoglobulin C-2 Type

smart00179
Location:4842 → 4881

EGF_CA; Calcium-binding EGF-like domain

smart00409
Location:792 → 879

IG; Immunoglobulin

smart00410
Location:2954 → 3034

IG_like; Immunoglobulin like

pfam07679
Location:4323 → 4409

I-set; Immunoglobulin I-set domain

pfam07474
Location:4411 → 4593

G2F; G2F domain

pfam07645
Location:4692 → 4733

EGF_CA; Calcium-binding EGF domain

pfam13519
Location:39 → 209

VWA_2; von Willebrand factor type A domain

cl11960
Location:4322 → 4405

Ig; Immunoglobulin domain
XM_011518467.3 → XP_011516769.1 hemicentin-2 isoform X3

Conserved Domains (11) summary

cd00096
Location:715 → 779

Ig; Immunoglobulin domain

smart00408
Location:4188 → 4250

IGc2; Immunoglobulin C-2 Type

smart00179
Location:4824 → 4863

EGF_CA; Calcium-binding EGF-like domain

smart00409
Location:792 → 879

IG; Immunoglobulin

smart00410
Location:1258 → 1340

IG_like; Immunoglobulin like

pfam07679
Location:4264 → 4350

I-set; Immunoglobulin I-set domain

pfam07474
Location:4352 → 4534

G2F; G2F domain

pfam07645
Location:4674 → 4715

EGF_CA; Calcium-binding EGF domain

pfam13519
Location:39 → 209

VWA_2; von Willebrand factor type A domain

pfam14670
Location:4593 → 4628

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl11960
Location:4263 → 4346

Ig; Immunoglobulin domain
XM_011518468.3 → XP_011516770.1 hemicentin-2 isoform X4

Conserved Domains (11) summary

cd00096
Location:1912 → 1975

Ig; Immunoglobulin domain

smart00408
Location:4247 → 4309

IGc2; Immunoglobulin C-2 Type

smart00179
Location:4689 → 4732

EGF_CA; Calcium-binding EGF-like domain

smart00409
Location:792 → 879

IG; Immunoglobulin

smart00410
Location:3329 → 3410

IG_like; Immunoglobulin like

pfam07679
Location:4323 → 4409

I-set; Immunoglobulin I-set domain

pfam07474
Location:4411 → 4593

G2F; G2F domain

pfam07645
Location:4733 → 4774

EGF_CA; Calcium-binding EGF domain

pfam13519
Location:39 → 209

VWA_2; von Willebrand factor type A domain

pfam14670
Location:4652 → 4687

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl11960
Location:4322 → 4405

Ig; Immunoglobulin domain
XM_011518469.3 → XP_011516771.1 hemicentin-2 isoform X6

Conserved Domains (7) summary

cd00096
Location:1912 → 1975

Ig; Immunoglobulin domain

smart00408
Location:1360 → 1423

IGc2; Immunoglobulin C-2 Type

smart00409
Location:792 → 879

IG; Immunoglobulin

smart00410
Location:1258 → 1340

IG_like; Immunoglobulin like

pfam07679
Location:3038 → 3129

I-set; Immunoglobulin I-set domain

pfam13519
Location:39 → 209

VWA_2; von Willebrand factor type A domain

cl11960
Location:2868 → 2942

Ig; Immunoglobulin domain
XM_011518470.3 → XP_011516772.1 hemicentin-2 isoform X7

Conserved Domains (7) summary

cd00096
Location:1912 → 1975

Ig; Immunoglobulin domain

smart00408
Location:1360 → 1423

IGc2; Immunoglobulin C-2 Type

smart00409
Location:792 → 879

IG; Immunoglobulin

smart00410
Location:2558 → 2638

IG_like; Immunoglobulin like

pfam07679
Location:608 → 692

I-set; Immunoglobulin I-set domain

pfam13519
Location:39 → 209

VWA_2; von Willebrand factor type A domain

cl11960
Location:2868 → 2942

Ig; Immunoglobulin domain
XM_017014585.2 → XP_016870074.1 hemicentin-2 isoform X5
XM_017014586.1 → XP_016870075.1 hemicentin-2 isoform X8

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

142470624..142639100

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054362616.1 → XP_054218591.1 hemicentin-2 isoform X2
XM_054362615.1 → XP_054218590.1 hemicentin-2 isoform X1
XM_054362617.1 → XP_054218592.1 hemicentin-2 isoform X3
XM_054362618.1 → XP_054218593.1 hemicentin-2 isoform X4
XM_054362620.1 → XP_054218595.1 hemicentin-2 isoform X6
XM_054362621.1 → XP_054218596.1 hemicentin-2 isoform X7
XM_054362619.1 → XP_054218594.1 hemicentin-2 isoform X5
XM_054362622.1 → XP_054218597.1 hemicentin-2 isoform X8

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_144655.1: Suppressed sequence

Description

NM_144655.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.